Change indexing of all MEAM element arrays (bb47fa87) · Commits · 郑智淋 / lammps

src/USER-MEAMC/meam.h

+25 −25

Original line number	Diff line number	Diff line
		@@ -62,21 +62,21 @@ class MEAM {
		// nr,dr = pair function discretization parameters
		// nrar,rdrar = spline coeff array parameters

		double Ec_meam[maxelt + 1][maxelt + 1], re_meam[maxelt + 1][maxelt + 1];
		double Omega_meam[maxelt + 1], Z_meam[maxelt + 1];
		double A_meam[maxelt + 1], alpha_meam[maxelt + 1][maxelt + 1],
		rho0_meam[maxelt + 1];
		double delta_meam[maxelt + 1][maxelt + 1];
		double beta0_meam[maxelt + 1], beta1_meam[maxelt + 1];
		double beta2_meam[maxelt + 1], beta3_meam[maxelt + 1];
		double t0_meam[maxelt + 1], t1_meam[maxelt + 1];
		double t2_meam[maxelt + 1], t3_meam[maxelt + 1];
		double rho_ref_meam[maxelt + 1];
		int ibar_meam[maxelt + 1], ielt_meam[maxelt + 1];
		lattice_t lattce_meam[maxelt + 1][maxelt + 1];
		int nn2_meam[maxelt + 1][maxelt + 1];
		int zbl_meam[maxelt + 1][maxelt + 1];
		int eltind[maxelt + 1][maxelt + 1];
		double Ec_meam[maxelt][maxelt], re_meam[maxelt][maxelt];
		double Omega_meam[maxelt], Z_meam[maxelt];
		double A_meam[maxelt], alpha_meam[maxelt][maxelt],
		rho0_meam[maxelt];
		double delta_meam[maxelt][maxelt];
		double beta0_meam[maxelt], beta1_meam[maxelt];
		double beta2_meam[maxelt], beta3_meam[maxelt];
		double t0_meam[maxelt], t1_meam[maxelt];
		double t2_meam[maxelt], t3_meam[maxelt];
		double rho_ref_meam[maxelt];
		int ibar_meam[maxelt], ielt_meam[maxelt];
		lattice_t lattce_meam[maxelt][maxelt];
		int nn2_meam[maxelt][maxelt];
		int zbl_meam[maxelt][maxelt];
		int eltind[maxelt][maxelt];
		int neltypes;

		double **phir;
		@@ -84,12 +84,12 @@ class MEAM {
		double phirar, phirar1, phirar2, phirar3, phirar4, phirar5,
		**phirar6;

		double attrac_meam[maxelt + 1][maxelt + 1],
		repuls_meam[maxelt + 1][maxelt + 1];
		double attrac_meam[maxelt][maxelt],
		repuls_meam[maxelt][maxelt];

		double Cmin_meam[maxelt + 1][maxelt + 1][maxelt + 1];
		double Cmax_meam[maxelt + 1][maxelt + 1][maxelt + 1];
		double rc_meam, delr_meam, ebound_meam[maxelt + 1][maxelt + 1];
		double Cmin_meam[maxelt][maxelt][maxelt];
		double Cmax_meam[maxelt][maxelt][maxelt];
		double rc_meam, delr_meam, ebound_meam[maxelt][maxelt];
		int augt1, ialloy, mix_ref_t, erose_form;
		int emb_lin_neg, bkgd_dyn;
		double gsmooth_factor;
		@@ -165,15 +165,15 @@ public:

		#define setall2d(arr, v) \
		{ \
		for (int __i = 1; __i <= maxelt; __i++) \
		for (int __j = 1; __j <= maxelt; __j++) \
		for (int __i = 0; __i < maxelt; __i++) \
		for (int __j = 0; __j < maxelt; __j++) \
		arr[__i][__j] = v; \
		}
		#define setall3d(arr, v) \
		{ \
		for (int __i = 1; __i <= maxelt; __i++) \
		for (int __j = 1; __j <= maxelt; __j++) \
		for (int __k = 1; __k <= maxelt; __k++) \
		for (int __i = 0; __i < maxelt; __i++) \
		for (int __j = 0; __j < maxelt; __j++) \
		for (int __k = 0; __k < maxelt; __k++) \
		arr[__i][__j][__k] = v; \
		}

src/USER-MEAMC/meam_dens_final.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -33,8 +33,8 @@ MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global,
		// Complete the calculation of density

		for (i = 1; i <= *nlocal; i++) {
		elti = arr1v(fmap, arr1v(type, i));
		if (elti > 0) {
		elti = fmap[arr1v(type, i)];
		if (elti >= 0) {
		arr1v(rho1, i) = 0.0;
		arr1v(rho2, i) = -1.0 / 3.0 * arr1v(arho2b, i) * arr1v(arho2b, i);
		arr1v(rho3, i) = 0.0;

src/USER-MEAMC/meam_dens_init.cpp

+14 −14

Original line number	Diff line number	Diff line
		@@ -135,9 +135,9 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair,
		double rnorm, fc, dfc, drinv;

		drinv = 1.0 / this->delr_meam;
		elti = arr1v(fmap, arr1v(type, i));
		elti = fmap[arr1v(type, i)];

		if (elti > 0) {
		if (elti >= 0) {

		xitmp = arr2v(x, 1, i);
		yitmp = arr2v(x, 2, i);
		@@ -146,8 +146,8 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair,
		for (jn = 1; jn <= numneigh; jn++) {
		j = arr1v(firstneigh, jn);

		eltj = arr1v(fmap, arr1v(type, j));
		if (eltj > 0) {
		eltj = fmap[arr1v(type, j)];
		if (eltj >= 0) {

		// First compute screening function itself, sij
		xjtmp = arr2v(x, 1, j);
		@@ -180,8 +180,8 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair,
		k = arr1v(firstneigh_full, kn);
		if (k == j)
		continue;
		eltk = arr1v(fmap, arr1v(type, k));
		if (eltk == 0)
		eltk = fmap[arr1v(type, k)];
		if (eltk < 0)
		continue;
		xktmp = arr2v(x, 1, k);
		yktmp = arr2v(x, 2, k);
		@@ -252,7 +252,7 @@ MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x,
		double ro0i, ro0j;
		double rhoa0i, rhoa1i, rhoa2i, rhoa3i, A1i, A2i, A3i;

		elti = arr1v(fmap, arr1v(type, i));
		elti = fmap[arr1v(type, i)];
		xtmp = arr2v(x, 1, i);
		ytmp = arr2v(x, 2, i);
		ztmp = arr2v(x, 3, i);
		@@ -265,7 +265,7 @@ MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x,
		delij[3] = arr2v(x, 3, j) - ztmp;
		rij2 = delij[1] * delij[1] + delij[2] * delij[2] + delij[3] * delij[3];
		if (rij2 < this->cutforcesq) {
		eltj = arr1v(fmap, arr1v(type, j));
		eltj = fmap[arr1v(type, j)];
		rij = sqrt(rij2);
		ai = rij / this->re_meam[elti][elti] - 1.0;
		aj = rij / this->re_meam[eltj][eltj] - 1.0;
		@@ -379,15 +379,15 @@ MEAM::screen(int i, int j, double** x, double rijsq, double* sij,
		double Cmax, Cmin, rbound;

		*sij = 1.0;
		eltj = arr1v(fmap, arr1v(type, j));
		elti = arr1v(fmap, arr1v(type, j));
		eltj = fmap[arr1v(type, j)];
		elti = fmap[arr1v(type, j)];

		// if rjksq > ebound*rijsq, atom k is definitely outside the ellipse
		rbound = this->ebound_meam[elti][eltj] * rijsq;

		for (nk = 1; nk <= numneigh_full; nk++) {
		k = arr1v(firstneigh_full, nk);
		eltk = arr1v(fmap, arr1v(type, k));
		eltk = fmap[arr1v(type, k)];
		if (k == j)
		continue;
		delxjk = arr2v(x, 1, k) - arr2v(x, 1, j);
		@@ -451,9 +451,9 @@ MEAM::dsij(int i, int j, int k, int jn, int numneigh, double rij2,
		double Cmax, Cmin, dCikj1, dCikj2;

		sij = arr1v(scrfcn, jn) * arr1v(fcpair, jn);
		elti = arr1v(fmap, arr1v(type, i));
		eltj = arr1v(fmap, arr1v(type, j));
		eltk = arr1v(fmap, arr1v(type, k));
		elti = fmap[arr1v(type, i)];
		eltj = fmap[arr1v(type, j)];
		eltk = fmap[arr1v(type, k)];
		Cmax = this->Cmax_meam[elti][eltj][eltk];
		Cmin = this->Cmin_meam[elti][eltj][eltk];

src/USER-MEAMC/meam_force.cpp

+8 −8

Original line number	Diff line number	Diff line
		@@ -74,9 +74,9 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,

		// Compute forces atom i

		elti = arr1v(fmap, arr1v(type, i));
		elti = fmap[arr1v(type, i)];

		if (elti > 0) {
		if (elti >= 0) {
		xitmp = arr2v(x, 1, i);
		yitmp = arr2v(x, 2, i);
		zitmp = arr2v(x, 3, i);
		@@ -84,9 +84,9 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
		// Treat each pair
		for (jn = 1; jn <= *numneigh; jn++) {
		j = arr1v(firstneigh, jn);
		eltj = arr1v(fmap, arr1v(type, j));
		eltj = fmap[arr1v(type, j)];

		if (!iszero(arr1v(scrfcn, fnoffset + jn)) && eltj > 0) {
		if (!iszero(arr1v(scrfcn, fnoffset + jn)) && eltj >= 0) {

		sij = arr1v(scrfcn, fnoffset + jn) * arr1v(fcpair, fnoffset + jn);
		delij[1] = arr2v(x, 1, j) - xitmp;
		@@ -98,7 +98,7 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
		r = rij;

		// Compute phi and phip
		ind = this->eltind[elti][eltj] - 1; //: TODO Remove -1 when reindexing eltind
		ind = this->eltind[elti][eltj];
		pp = rij * this->rdrar;
		kk = (int)pp;
		kk = std::min(kk, this->nrar - 2);
		@@ -514,8 +514,8 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
		continue; //: cont jn loop
		for (kn = 1; kn <= *numneigh_full; kn++) {
		k = arr1v(firstneigh_full, kn);
		eltk = arr1v(fmap, arr1v(type, k));
		if (k != j && eltk > 0) {
		eltk = fmap[arr1v(type, k)];
		if (k != j && eltk >= 0) {
		dsij(i, j, k, jn, numneigh, rij2, &dsij1, &dsij2, ntype,
		type, fmap, x, &scrfcn[fnoffset], &fcpair[fnoffset]);
		if (!iszero(dsij1) \|\| !iszero(dsij2)) {
		@@ -579,6 +579,6 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
		// end of j loop
		}

		// else if elti=0, this is not a meam atom
		// else if elti<0, this is not a meam atom
		}
		}

src/USER-MEAMC/meam_setup_done.cpp

+16 −16

Original line number	Diff line number	Diff line
		@@ -26,7 +26,7 @@ MEAM::meam_setup_done(double* cutmax)
		*cutmax = this->cutforce;

		// Augment t1 term
		for (int i = 1; i <= maxelt; i++)
		for (int i = 0; i < maxelt; i++)
		this->t1_meam[i] =
		this->t1_meam[i] + this->augt1 * 3.0 / 5.0 * this->t3_meam[i];

		@@ -71,9 +71,9 @@ MEAM::meam_setup_done(double* cutmax)
		this->v3D[9] = 3;
		this->v3D[10] = 1;

		nv2 = 1;
		for (m = 1; m <= this->neltypes; m++) {
		for (n = m; n <= this->neltypes; n++) {
		nv2 = 0;
		for (m = 0; m < this->neltypes; m++) {
		for (n = m; n < this->neltypes; n++) {
		this->eltind[m][n] = nv2;
		this->eltind[n][m] = nv2;
		nv2 = nv2 + 1;
		@@ -99,8 +99,8 @@ MEAM::alloyparams(void)
		double eb;

		// Loop over pairs
		for (i = 1; i <= this->neltypes; i++) {
		for (j = 1; i <= this->neltypes; i++) {
		for (i = 0; i < this->neltypes; i++) {
		for (j = 0; i < this->neltypes; i++) {
		// Treat off-diagonal pairs
		// If i>j, set all equal to i<j case (which has aready been set,
		// here or in the input file)
		@@ -144,9 +144,9 @@ MEAM::alloyparams(void)

		// Cmin[i][k][j] is symmetric in i-j, but not k. For all triplets
		// where i>j, set equal to the i<j element. Likewise for Cmax.
		for (i = 2; i <= this->neltypes; i++) {
		for (j = 1; j <= i - 1; j++) {
		for (k = 1; k <= this->neltypes; k++) {
		for (i = 1; i < this->neltypes; i++) {
		for (j = 0; j < i; j++) {
		for (k = 0; k < this->neltypes; k++) {
		this->Cmin_meam[i][j][k] = this->Cmin_meam[j][i][k];
		this->Cmax_meam[i][j][k] = this->Cmax_meam[j][i][k];
		}
		@@ -157,9 +157,9 @@ MEAM::alloyparams(void)
		// atom k definitely lies outside the screening function ellipse (so
		// there is no need to calculate its effects). Here, compute it for all
		// triplets [i][j][k] so that ebound[i][j] is the maximized over k
		for (i = 2; i <= this->neltypes; i++) {
		for (j = 1; j <= this->neltypes; j++) {
		for (k = 1; k <= this->neltypes; k++) {
		for (i = 0; i < this->neltypes; i++) {
		for (j = 0; j < this->neltypes; j++) {
		for (k = 0; k < this->neltypes; k++) {
		eb = (this->Cmax_meam[i][j][k] * this->Cmax_meam[i][j][k]) /
		(4.0 * (this->Cmax_meam[i][j][k] - 1.0));
		this->ebound_meam[i][j] = std::max(this->ebound_meam[i][j], eb);
		@@ -241,8 +241,8 @@ MEAM::compute_pair_meam(void)

		// loop over pairs of element types
		nv2 = 0;
		for (a = 1; a <= this->neltypes; a++) {
		for (b = a; b <= this->neltypes; b++) {
		for (a = 0; a < this->neltypes; a++) {
		for (b = a; b < this->neltypes; b++) {
		// loop over r values and compute
		for (j = 0; j < this->nr; j++) {
		r = j * this->dr;
		@@ -593,7 +593,7 @@ MEAM::compute_reference_density(void)
		double rho0, rho0_2nn, arat, scrn;

		// loop over element types
		for (a = 1; a <= this->neltypes; a++) {
		for (a = 0; a < this->neltypes; a++) {
		Z = (int)this->Z_meam[a];
		if (this->ibar_meam[a] <= 0)
		Gbar = 1.0;

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